Quantifying space use and segregation, as well as the extrinsic and intrinsic factors affecting them, is crucial to increase our knowledge of species-specific movement ecology and to design effective management and conservation measures. This is particularly relevant in the case of species that are highly mobile and dependent on sparse and unpredictable trophic resources, such as vultures. Here, we used the GPS-tagged data of 127 adult Griffon Vultures Gyps fulvus captured at five different breeding regions in Spain to describe the movement patterns (home-range size and fidelity, and monthly cumulative distance). We also examined how individual sex, season and breeding region determined the cumulative distance travelled and the size and overlap between consecutive monthly home-ranges. Overall, Griffon Vultures exhibited very large annual home-range sizes of 5,027 ± 2,123 km2, mean monthly cumulative distances of 1,776 ± 1,497 km, and showed a monthly home-range fidelity of 67.8 ± 25.5 %. However, individuals from northern breeding regions showed smaller home-ranges and travelled shorter monthly distances than those from southern ones. In all cases, home-ranges were larger in spring and summer than in winter and autumn. Moreover, females showed larger home-ranges and less monthly fidelity than males, indicating that the latter tended to use the similar areas throughout the year. Overall, our results indicate that both extrinsic and intrinsic factors modulate the home-range the social Griffon Vulture and that spatial segregation depend on sex and season at the individual level, without relevant differences between breeding regions in individual site fidelity.
Phenotypic divergence is an important consequence of restricted gene flow in insular populations. This divergence can be challenging to detect when it occurs through subtle shifts in morphological traits, particularly in traits with complex geometries, like insect wing venation. Here, we employed geometric morphometrics to assess the extent of variation in wing venation patterns across reproductively isolated populations of the social sweat bee, Halictus tripartitus. We examined wing morphology of specimens sampled from a reproductively isolated population of H. tripartitus on Santa Cruz Island (Channel Islands, Southern California). Our analysis revealed significant differentiation in wing venation in this island population relative to conspecific mainland populations. We additionally found that this population-level variation was less pronounced than the species-level variation in wing venation among three sympatric congeners native to the region, Halictus tripartitus, Halictus ligatus, and Halictus farinosus. Together, these results provide evidence for subtle phenotypic divergence in an island bee population. More broadly, these results emphasize the utility and potential of wing morphometrics for large-scale assessment of insect population structure.
A combination of short-read paired-end and mate-pair libraries of large insert sizes is used as a standard method to generate genome assemblies with high contiguity. The third-generation sequencing techniques also are used to improve the quality of assembled genomes. However, both mate-pair libraries and the third-generation libraries require high-molecular-weight DNA, making the use of these libraries inappropriate for samples with only degraded DNA. An in silico method that generates mate-pair libraries using a reference genome was devised for the task of assembling target genomes. Although the contiguity and completeness of assembled genomes were significantly improved by this method, a high level of errors manifested in the assembly, further to which the methods for using reference genomes were not optimized. Here, we tested different strategies for using reference genomes to generate in silico mate-pairs. The results showed that using a closely related reference genome from the same genus was more effective than using divergent references. Conservation of in silico mate-pairs by comparing two references and using those to guide genome assembly reduced the number of misassemblies (18.6% – 46.1%) and increased the contiguity of assembled genomes (9.7% – 70.7%), while maintaining gene completeness at a level that was either similar or marginally lower than that obtained via the current method. Finally, we developed a pipeline of optimized method and compared it with another reference-guided assembler, Ragtag. We found that Ragtag produced longer scaffolds (17.8 Mbp vs. 3.0 Mbp), but resulted in a much higher misassembly rate (85.68%) than our optimized in silico mate-pair method. This optimized in silico pipeline developed in this study should facilitate further studies on genomics, population genetics and conservation of endangered species.
Conservation and management professionals often works across jurisdictional boundaries to identify broad ecological patterns. These collaborations help to protect populations whose distributions span political borders. One common limitation to multijurisdictional collaboration is consistency in data recording and reporting. This limitation can impact genetic research which relies on data about specific markers in an organism’s genome. Incomplete overlap of markers between separate studies can prevent direct comparisons. Standardized marker panels can reduce the impact this issue and provide a common starting place for new research. Genotyping-in-thousands (GTSeq) is one approach used to create standardized marker panels for non-model organisms. Here we describe the development, optimization, and early assessments of a new GTSeq panel for use with walleye (Sander vitreus) from the Great Lakes region of North America. High genome-coverage sequencing conducted using RAD-capture provided genotypes for thousands of single nucleotide polymorphisms (SNPs). From these markers, SNP and microhaplotype makers were chosen that were informative for genetic stock identification (GSI) and kinship analysis. The final GTSeq panel contained 500 markers, including 197 microhaplotypes and 303 SNPs. Leave-one-out GSI simulations indicated that GSI accuracy should be greater than 80% in most jurisdictions. The false-positive rates of parent-offspring and full-sibling kinship identification was found to be low. Finally, genotypes could be consistently scored among separate sequencing runs >94% of the time. Results indicate that the GTSeq panel we developed should perform well for multijurisdictional research throughout the Great Lakes region.
Siraitia grosvenorii, an economically important plant species with high medicinal value, is endemic to subtropical China. To determine the population structure and origin of cultivated S. grosvenorii, we examined the variation in three chloroplast DNA regions (trnR-atpA, trnH-psbA, trnL-trnF) and two nuclear gene orthologs (CHS and EDL2) of S. grosvenorii in 130 individuals, selected from 13 wild populations across its natural distribution range, and 21 cultivated accessions using a phylogeographic approach. The results showed non-overlapping distribution of chlorotypes, three distinct chloroplast genetic groups restricted to different mountain ranges, and comparable nuclear diversity among the distinct geographical groups, suggesting the existence of at least three separate refugia. The current phylogeographic patterns of S. grosvenorii probably resulted from long-term survival in multiple refugia and limited expansion. Our results also demonstrated that wild populations in northeastern Guangxi share the same gene pool as cultivated S. grosvenorii accessions, suggesting that the current cultivars originated from wild populations distributed in northeastern Guangxi. The results of this study provide insight into improving the efficiency of S. grosvenorii breeding using a genetic approach, and outline measures for the conservation of its genetic resources.
Ecuador has both high richness and high endemism of species which are increasingly threatened by anthropic pressures, including roads. However, research evaluating the effects of roads remains scarce, making it difficult to develop mitigation plans. Here we present the first national assessment of wildlife mortality that allow us to 1) identify species and areas where mortality occurs due to collision with vehicles and 2) reveal knowledge gaps. We bring together data from systematic surveys and citizen science efforts in Ecuador to present a dataset with >5000 wildlife roadkill records from 454 species. Systematic surveys were reported by ten studies conducted in five out of the 24 Ecuadorian provinces. Collectively they revealed 282 species with mortality rates ranging from 0.008 to 95.56 ind./km/year. The highest rates were for the yellow warbler Setophaga petechia in Galápagos (95.56 ind./km/year), the cane toad Rhinella marina in Napo (16.91 ind./km/year), and the small ground-finch Geospiza fuliginosa in Galápagos (14.11 ind./km/year). Citizen science and other no systematic monitoring provided 1705 roadkill records representing all the 24 provinces of Ecuador and 299 species. The common opossum Didelphis marsupialis, the Andean white-eared opossum Didelphis pernigra, and the yellow warbler Setophaga petechia were more commonly reported (250, 104, and 81 individuals respectively). Across all sources, we found 15 species listed as Threatened and six as Data Deficient by the IUCN. We suggest stronger research efforts on areas where mortality of endemic or threatened species could be critical for populations, such as in Galápagos. This first assessment of wildlife mortality on Ecuadorian roads represents contributions from several sectors including academia, members of the public, and government underlining the value of wider engagement and collaboration. We hope these findings and the compiled dataset will guide sustainable planning of infrastructure in Ecuador and ultimately, contribute to reduce wildlife mortality on roads.
Plant and soil biodiversity can have significant effects on herbivore resistance mediated by plant metabolites. Here, we disentangled the independent effects of plant diversity and soil legacy on constitutive and herbivore-induced plant metabolomes of three plant species in two complementary microcosm experiments. First, we grew plants in sterile soil with three different plant diversity levels. Second, single plant species were grown on soil with different plant diversity-induced soil legacies. We infested a subset of all plants with Spodoptera exigua larvae, a generalist leaf-chewing herbivore, and assessed foliar and root metabolomes. Neither plant diversity nor soil legacy had significant effects on overall foliar, root, or herbivore-induced metabolome composition. Herbivore-induced metabolomes, however, differed from those of control plants. We also detected 139 significantly regulated metabolites by comparing plants grown in monocultures with conspecifics growing in plant or soil legacy mixtures. Moreover, plant-plant and plant-soil interactions regulated 141 metabolites in herbivore-induced plants. Taken together, plant diversity and soil legacy independently alter the concentration and induction of plant metabolites, thus affecting the plant's defensive capability. This is a first step towards disentangling plant and soil biodiversity effects on herbivore resistance, thereby improving our understanding of the mechanisms that govern ecosystem functioning.
1. Describing and explaining patterns of individual animal behaviors in situ, and their repeatability over the annual cycle, is an emerging field in ecology owing largely to advances in tagging technology. 2. We describe individual movements of adult Sakhalin taimen Parahucho perryi, an endangered salmonid fish, in the headwaters of a river in northern Japan during the spring spawning season over two years. 3. Migration timing, separated into stages prior to, during, and following the spawning period, was found to be more consistent and repeatable for females than males. 4. We hypothesized that the observed coordinated movement within seasons, and repeatability in migration timing across seasons, could result from 1) individual-specific responsiveness resulting from endogenous, biological traits that are mediated by environmental factors, or 2) social interactions among comigrating individuals. 5. We found that water temperature and water level experienced by fish near the river mouth approximately a week before arrival at the spawning ground explained variability in run timing between years for females but not males. 6. We found no evidence of conspecific attraction or repulsion resulting from social interactions among the spawners and post-spawners. 7. We conclude that individual-specific responsiveness to environmental cues was the likely mechanism underpinning the observed migration timing and movement patterns. 8. Determining the importance of these environmental and social factors not only during spawning but also during non-breeding life-history stages would contribute to a more comprehensive understanding of migratory connectivity in this species.
Myriad ecological and evolutionary factors can influence whether a particular parasite successfully transmits to a new host during a disease outbreak, with consequences for the structure and diversity of parasite populations. However, even though the diversity and evolution of parasite populations is of clear fundamental and applied importance, we have surprisingly few studies that track how genetic structure of parasites changes during naturally occurring outbreaks in non-human populations. Here, we used population genetic approaches to reveal how genotypes of a bacterial parasite, Pasteuria ramosa, change over time, focusing on how infecting P. ramosa genotypes change during the course of epidemics in Daphnia populations in two lakes. We found evidence for genetic change – and, therefore, evolution – of the parasite during outbreaks. In one lake, P. ramosa genotypes structured by sampling date; in both lakes, genetic distance between groups of P. ramosa isolates increased with time between sampling. Diversity in parasite populations remained constant over epidemics, though one epidemic (which was large) had low genetic diversity while the other epidemic (which was small) had high genetic diversity. Our findings demonstrate that patterns of parasite evolution differ between outbreaks; future studies exploring the feedbacks between epidemic size, host diversity, and parasite genetic diversity would improve our understanding of parasite dynamics and evolution.
Automated 3D-image based tracking systems are new and promising devices to investigate the foraging behaviour of flying animals with great accuracy and precision. 3D analyses can provide accurate assessments of flight performance in regard to speed, curvature, and hovering. However, there have been few applications of this technology in ecology, particularly for insects. We used this technology to analyse the behavioural interactions between the Western honey bee Apis melifera and its invasive predator the Asian hornet, Vespa velutina nigrithorax. We investigated whether predation success could be affected by flight speed, flight curvature, and hovering of the Asian hornet and honey bees in front of one beehive. We recorded a total of 603,259 flight trajectories and 5,175 predator-prey flight interactions leading to 126 successful predation events, representing 2.4% predation success. Flight speeds of hornets in front of hive entrances were much lower than that of their bee prey; in contrast to hovering capacity, while curvature range overlapped between the two species. There were large differences in speed, curvature and hovering between the exit and entrance flights of honey bees. Interestingly, we found hornet density affected flight performance of both honey bees and hornets. Higher hornet density led to a decrease in the speed of honey bees leaving the hive, and an increase in the speed of honey bees entering the hive, together with more curved flight trajectories. These effects suggest some predator avoidance behaviour by the bees. Higher honey bee flight curvature resulted in lower hornet predation success. Results showed an increase of predation success when hornet number increased up to 8 individuals, above which predation success decreased, likely due to competition among predators. Although based on a single colony, this study reveals interesting outcomes derived from the use of automated 3D tracking to derive accurate measures of individual behaviour and behavioural interactions among flying species.
1. The Environmental Data Initiative (EDI) is a trustworthy, stable data repository and data management support organization for the environmental scientist. In a bottom-up community process EDI was built with the premise that freely and easily available data are necessary to advance the understanding of complex environmental processes and change, to improve transparency of research results, and to democratize ecological research. 2. EDI provides tools and support that allow the environmental researcher to easily integrate data publishing into the research workflow. 3. Almost ten years since going into production, we analyze metadata to provide a general description of EDI’s collection of data and its data management philosophy and placement in the repository landscape. We discuss how comprehensive metadata and the repository infrastructure lead to highly findable, accessible, interoperable, and reusable (FAIR) data by evaluating compliance with specific community proposed FAIR criteria. 4. Finally, we review measures and patterns of data (re)use, assuring that EDI is fulfilling its stated premise.
Plasmids are extra-chromosomal genetic elements that encode a wide variety of phenotypes and can be maintained in bacterial populations through vertical and horizontal transmission, thus increasing bacterial adaptation to hostile environmental conditions like those imposed by antimicrobial substances. To circumvent the segregational instability resulting from randomly distributing plasmids between daughter cells upon division, non-transmissible plasmids tend to be carried in multiple copies per cell, which also results in a metabolic burden to the bacterial host, therefore reducing the overall fitness. This trade-off poses an existential question for plasmids: What is the optimal plasmid copy number? We address this question using a combination of population genetics modeling with microbiology experiments consisting of Escherichia coli K12 bearing a multi-copy plasmid encoding for blaTEM-1, a gene conferring resistance to b-lactam antibiotics. We use a Wright-Fisher model to evaluate the interaction between the above mentioned opposing forces. By numerically determining the optimal plasmid copy number for constant and fluctuating selection regimes, we conclude that plasmid copy number is an optimized evolutionary trait that depends on the rate of environmental fluctuation and balances the benefit between increased stability in the absence of selection with the burden associated with carrying multiple copies of the plasmid.
The National Forestry Commission of Mexico continuously monitors forest structure within the country’s continental territory by the implementation of the National Forest and Soils Inventory (INFyS). Due to the challenges involved in collecting data exclusively from field surveys, there are spatial information gaps for important forest attributes. This can produce bias or increase uncertainty when generating estimates required to support forest management decisions. Our objective is to predict the spatial distribution of tree height and tree density in all Mexican forests. We performed wall-to-wall spatial predictions of both attributes in 1-km grids, using ensemble machine learning across each forest type in Mexico. Predictor variables include remote sensing imagery and other geospatial data (e.g., vegetation indexes, surface temperature). Training data is from the 2009-2014 cycle (n>26,000 sampling plots). Spatial cross validation suggested that the model had a better performance when predicting tree height r2=0.4 [0.15,0.55] (mean[min, max]) than for tree density r2=0.2[0.10,0.31]. Maximum values of tree height were for coniferous forests, coniferous-broadleaf forests and cloud mountain forest (~36 m, 30 m and 21 m, respectively). Tropical forests had maximum values of tree density (~1370 trees/ha), followed by tropical dry forest (1006 trees/ha) and coniferous forest (988 trees/ha). Although most forests had relatively low values of uncertainty, e.g., values <40%, arid and semiarid ecosystems had high uncertainty in both tree height and tree density predictions, e.g., values >60%. The applied open science approach we present is easily replicable and scalable, thus it is helpful to assist in the decision-making and future of the National Forest and Soils Inventory. This work highlights the need for technical capabilities aimed to use and resignify all the effort done by the Mexican Forestry Commission in implementing the INFyS.
Designing appropriate management plans requires knowledge of both the dispersal ability and what has shaped the current distribution of the species under consideration. Here we investigated the evolutionary history of the endangered grey reef shark (Carcharhinus amblyrhynchos) across its range by sequencing thousands of RAD-seq loci in 173 individuals in the Indo-Pacific (IP) . We first bring evidence of the occurrence of a range expansion (RE) originating close to the Indo-Australian Archipelago (IAA) where two stepping-stone waves (east and westward) colonized almost the entire IP. Coalescent modeling additionally highlighted a homogenous connectivity (Nm~10 per generation) throughout the range, and an isolation by distance model suggested the absence of barriers to dispersal despite the affinity of C. amblyrhynchos to coral reefs. This coincides with long-distance swims previously recorded, suggesting that the strong genetic structure at the IP scale (FST ~ 0.56 between its ends) is the consequence of its broad current distribution and organization in a large number of demes. Our results strongly suggest that management plans for the grey reef shark should be designed on a range-wide rather than a local scale due to its continuous genetic structure. We further contrasted these results with those obtained previously for the sympatric but strictly lagoon-associated Carcharhinus melanopterus, known for its restricted dispersal ability. C. melanopterus exhibits similar RE dynamic, but is characterized by stronger genetic structure and a non-homogeneous connectivity largely dependent on local coral reefs availability. This sheds new light on shark evolution, emphasizing the roles of IAA as source of biodiversity and of life history traits in shaping the extent of genetic structure and diversity.
Terrestrial resource pulses can significantly affect the community dynamics of freshwater ecosystems. Previously, its effect on the river community is considered to be stronger in summer, while weaker in winter when terrestrial invertebrates are less abundant. The movement of the terrestrial earthworms are triggered in winter, so they may be supplied to winter rivers as terrestrial resource pulse, but little is known about it. Here, we report that the massive numbers of the terrestrial earthworms were supplied intensively to an upstream of the small river in early winter. In particular, we found large numbers of Megascolecidae earthworms were supplied in an upstream of the small river in Northern Japan. Furthermore, we observed that supplied earthworms were consumed by salmonid fish species (masu salmon, white spotted char and rainbow trout) and aquatic invertebrates (gammarid amphipod, planarian flatworm and stonefly larvae). These findings suggests that the terrestrial earthworms may play a key role in ecosystem functioning in winter when severe and other resources are scarce.
In many species, offspring display conspicuous adult-like colouration already early in life, even though they might be very vulnerable to predation at this stage. Yet, the signalling function of adult-like traits in nestlings has been little explored to date. Here, we investigated whether the yellow breast plumage of blue tit (Cyanistes caeruleus) nestlings shows patterns of condition-dependence and hence signals individual quality, as has been described for adult birds. During three consecutive breeding seasons, we therefore explored the association between nestling body mass and three colour components of the yellow breast plumage (i.e., UV chroma, carotenoid chroma and total brightness), considering both within and among nest effects. Carotenoid chroma was not affected by body mass. However, UV chroma and total brightness showed an among-nest effect of body mass, suggesting that they might signal aspects of genetic quality or parental rearing capacity. Interestingly, we also found a within-nest effect of body mass on total brightness, suggesting that this is a good candidate for a condition-dependent signal within the family. Thus, other family members could rely on brightness to adjust their behavioural strategies, such as feeding behaviour in parents. Our study thus reveals that certain colour components of the yellow breast plumage signal different aspects of offspring quality and suggest that they might have a correlated signalling value across life-history stages.